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by: Haylie Satterfield

Bioinformatics CISC436

Haylie Satterfield
GPA 3.84


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This 9 page Study Guide was uploaded by Haylie Satterfield on Saturday September 19, 2015. The Study Guide belongs to CISC436 at University of Delaware taught by LiLiao in Fall. Since its upload, it has received 36 views. For similar materials see /class/207172/cisc436-university-of-delaware in Computer Information Technology at University of Delaware.

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Date Created: 09/19/15
CISC 436636 Intro to Bioinformatics Spring 2008 Review Session Basics of Molecular biology 0 Central dogma Transcription Translation Genetic code 0 DNA Double helix WatsonCrick binding 0 RNA Secondary structures 0 Genes Compositional Structure Reading frames 0 Proteins Secondary structure alpha helices beta sheets and coils 3d structure 0 Gene Regulations Operons DNA Microarray Cloning 0 PCR 0 Gel electrophoresis 0 2D gel MS 0 Yeast 2 hybrid system Computational methods Dynamic programming 7 Problems can be dissect to subproblems 7 Recurrence equations 7 DP Table 7 Traceback Maximum Likelihood Pairwise alignments Multiple alignments Hidden Markov models Viterbi forward and Viterbi training Phylogenetic trees distancebased characterbased and probabilitybased Bootstrap Structural predictions secondary lattice model Clustering Profiles and inferring genetic networks Kmeans Boolean networks Phylogenetic Trees Motivations Concepts and assumptions Gene trees versus species trees Rooted vs unrooted Mothods Characterbased 0 Maximum Parsimony conventional and weighted Traceback Distancebased UWPGA Neighborjoining Metric distance ultrametric distance molecular clock additive distance Probabilitybased Evolution models JukesCantor Kimura RNA secondary structures Concepts Single strand Intramolecular pairings Structural categories Hairpins bulge loops interior loops and multi loops Pseudo knots Similarity in secondary structure plays a more important role than primary sequence in determining homology for RNAs Algorithms for predicting structures Nussinov s 0 Maximum base pairing Zuker s Minimum energy Protein structures Concepts An nsen hypothesis Primary secondary tertiary and quaternary Algorithms for predicting structures Secondary structure encoding Artificial neural networks 3dimensional Lattice models HP models Genetic algorithm Genetic networks Concepts Regulation proteinprotein interactions Operons Clustering and Modeling Kmean Boolean networks Acyclic Truth tables 0 3 steps predictor Maximum entropy chooser About the Final Exam Time and Place May 29 1030AM1230AM Kirkbride 205 closedbook Four parts Primary sequence analysis 30 points Phylogenetic trees 30 points Structural prediction 25 points Clustering gene expression pro les Kmeans and inferring genetic network 15 points Thank you and hope to see you in CISC841


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